The 'contingency' supply of 400,000 doses will be made available during the flu season if local stocks run dry, as they did in England last winter.
The government's director of immunisation Professor David Salisbury described the measure as an 'insurance policy' but denied that it meant the DoH had no faith in GPs to order sufficient quantities of vaccine.
'We need to be prepared against all eventualities,' he said. 'It might not be used; we hope it isn't used. We put in the order as a contingency.'
The DoH has held a consultation on its plans to strip GPs of flu vaccine-ordering duties, which ended in August.
At a briefing at the DoH in London on Thursday, CMO Professor Sally Davies also revealed that regulations over prescribing of antivirals have been changed.
When given the go-ahead by the CMO, GPs will be able to prescribe Tamiflu and Relenza to patients not in at-risk groups when they believe patients may suffer complications from flu.
A contingency stockpile will allow the drugs to be released by the government if manufacturers' stocks run low.
GPs will also be alerted when they can no longer prescribe antivirals to such patients.
Dame Sally reiterated the department's stance on the lack of a flu vaccine awareness campaign for this winter, saying the DoH believed messages directly from health professionals were the best way to encourage greater uptake.
'We know from what people tell us that health professionals are the most trusted,' she said. 'That's why we are asking for GPs to be doing it.'
In addition, a targeted message will appear on prescription bags in 2,200 pharmacies in England for four weeks, starting 23 October.
Around 16.7 million doses of seasonal flu vaccine have been ordered for this winter, up from 14.7 million last season.